Magnesium in PDB 5jjl: Rho Transcription Termination Factor Bound to RU8 and 5 Adp-BEF3 Molecules

The structure of Rho Transcription Termination Factor Bound to RU8 and 5 Adp-BEF3 Molecules, PDB code: 5jjl was solved by N.D.Thomsen, M.R.Lawson, L.B.Witkowsky, S.Qu, J.M.Berger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.52 / 3.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.091, 199.071, 111.666, 90.00, 105.02, 90.00
R / Rfree (%)	23.2 / 26.6

The structure of Rho Transcription Termination Factor Bound to RU8 and 5 Adp-BEF3 Molecules also contains other interesting chemical elements:

Fluorine

(F)

15 atoms

The binding sites of Magnesium atom in the Rho Transcription Termination Factor Bound to RU8 and 5 Adp-BEF3 Molecules (pdb code 5jjl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Rho Transcription Termination Factor Bound to RU8 and 5 Adp-BEF3 Molecules, PDB code: 5jjl:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Rho Transcription Termination Factor Bound to RU8 and 5 Adp-BEF3 Molecules


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rho Transcription Termination Factor Bound to RU8 and 5 Adp-BEF3 Molecules within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:29.6 occ:1.00 O A:HOH1101 1.9 29.7 1.0 F3 A:BEF1002 1.9 58.9 1.0 O A:HOH1102 2.0 50.8 1.0 O A:HOH1103 2.0 51.7 1.0 O1B A:ADP1000 2.0 36.1 1.0 OG1 A:THR185 2.1 33.8 1.0 PB A:ADP1000 3.0 35.8 1.0 O2B A:ADP1000 3.1 34.8 1.0 CB A:THR185 3.2 34.7 1.0 BE A:BEF1002 3.3 58.6 1.0 O1A A:ADP1000 3.7 36.1 1.0 NH1 A:ARG212 3.8 35.9 1.0 N A:THR185 3.9 35.4 1.0 F2 A:BEF1002 4.0 58.6 1.0 OE2 A:GLU215 4.0 51.3 1.0 O3B A:ADP1000 4.0 36.0 1.0 CA A:THR185 4.1 35.6 1.0 O3A A:ADP1000 4.2 36.6 1.0 OE1 A:GLU215 4.3 51.6 1.0 CG2 A:THR185 4.3 35.2 1.0 PA A:ADP1000 4.3 37.0 1.0 OD2 A:ASP265 4.3 48.3 1.0 OD1 A:ASP265 4.4 47.6 1.0 F1 A:BEF1002 4.4 57.8 1.0 OE2 A:GLU211 4.5 48.2 1.0 CD A:GLU215 4.6 51.6 1.0 NH2 B:ARG366 4.6 35.2 1.0 O2A A:ADP1000 4.7 38.1 1.0 CB A:LYS184 4.8 42.7 1.0 CG A:ASP265 4.8 48.2 1.0 C A:LYS184 4.9 43.9 1.0 CD A:GLU211 4.9 48.6 1.0

Magnesium binding site 2 out of 5 in the Rho Transcription Termination Factor Bound to RU8 and 5 Adp-BEF3 Molecules


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Rho Transcription Termination Factor Bound to RU8 and 5 Adp-BEF3 Molecules within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1001 b:18.7 occ:1.00 O B:HOH1103 1.9 53.7 1.0 F3 B:BEF1002 1.9 46.6 1.0 O B:HOH1101 2.0 19.8 1.0 O1B B:ADP1000 2.0 28.2 1.0 O B:HOH1102 2.1 20.5 1.0 OG1 B:THR185 2.1 32.5 1.0 PB B:ADP1000 3.0 28.1 1.0 O2B B:ADP1000 3.1 28.1 1.0 CB B:THR185 3.2 33.3 1.0 BE B:BEF1002 3.3 46.4 1.0 O2A B:ADP1000 3.7 29.8 1.0 NH1 B:ARG212 3.8 22.0 1.0 N B:THR185 3.9 32.8 1.0 F2 B:BEF1002 4.0 45.7 1.0 O3B B:ADP1000 4.1 27.6 1.0 CA B:THR185 4.1 33.3 1.0 O3A B:ADP1000 4.2 29.0 1.0 OE1 B:GLU215 4.2 43.0 1.0 OE2 B:GLU215 4.2 43.5 1.0 OD2 B:ASP265 4.3 27.8 1.0 CG2 B:THR185 4.3 34.1 1.0 PA B:ADP1000 4.3 29.9 1.0 F1 B:BEF1002 4.4 46.6 1.0 OD1 B:ASP265 4.4 26.6 1.0 OE2 B:GLU211 4.5 32.1 1.0 CD B:GLU215 4.7 43.6 1.0 O1A B:ADP1000 4.7 30.2 1.0 CD B:GLU211 4.7 31.8 1.0 CG B:ASP265 4.8 27.2 1.0 OE1 B:GLU211 4.8 31.2 1.0 NH2 C:ARG366 4.8 21.6 1.0 CB B:LYS184 4.9 19.9 1.0 C B:LYS184 4.9 21.1 1.0

Magnesium binding site 3 out of 5 in the Rho Transcription Termination Factor Bound to RU8 and 5 Adp-BEF3 Molecules


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Rho Transcription Termination Factor Bound to RU8 and 5 Adp-BEF3 Molecules within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1001 b:49.8 occ:1.00 O C:HOH1104 1.9 24.4 1.0 F3 C:BEF1002 1.9 23.1 1.0 O C:HOH1101 2.0 25.3 1.0 OG1 C:THR185 2.0 32.8 1.0 O2B C:ADP1000 2.0 31.7 1.0 O C:HOH1103 2.1 43.5 1.0 PB C:ADP1000 3.0 31.9 1.0 CB C:THR185 3.1 34.0 1.0 O3B C:ADP1000 3.1 32.2 1.0 BE C:BEF1002 3.3 22.8 1.0 O2A C:ADP1000 3.7 35.0 1.0 NH1 C:ARG212 3.8 25.2 1.0 N C:THR185 3.8 32.7 1.0 F2 C:BEF1002 4.0 21.3 1.0 CA C:THR185 4.0 33.4 1.0 O1B C:ADP1000 4.1 30.8 1.0 OE2 C:GLU215 4.2 41.3 1.0 O3A C:ADP1000 4.2 33.4 1.0 OD2 C:ASP265 4.2 31.2 1.0 CG2 C:THR185 4.2 35.0 1.0 PA C:ADP1000 4.3 35.0 1.0 F1 C:BEF1002 4.4 23.5 1.0 NH2 D:ARG366 4.5 33.4 1.0 OE2 C:GLU211 4.5 41.7 1.0 OD1 C:ASP265 4.5 29.2 1.0 OE1 C:GLU215 4.6 40.0 1.0 O1A C:ADP1000 4.7 35.0 1.0 CD C:GLU215 4.7 41.3 1.0 CG C:ASP265 4.8 30.0 1.0 CB C:LYS184 4.9 34.1 1.0 C C:LYS184 4.9 36.1 1.0 CD C:GLU211 4.9 40.8 1.0 CZ C:ARG212 5.0 26.0 1.0

Magnesium binding site 4 out of 5 in the Rho Transcription Termination Factor Bound to RU8 and 5 Adp-BEF3 Molecules


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Rho Transcription Termination Factor Bound to RU8 and 5 Adp-BEF3 Molecules within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1001 b:80.7 occ:1.00 O D:HOH1101 1.7 58.7 1.0 F3 D:BEF1002 1.9 76.0 1.0 O2B D:ADP1000 2.0 53.9 1.0 O D:HOH1103 2.0 76.0 1.0 OG1 D:THR185 2.0 70.1 1.0 O D:HOH1102 2.1 42.6 1.0 CB D:THR185 2.7 72.6 1.0 PB D:ADP1000 3.0 53.9 1.0 O3B D:ADP1000 3.1 53.9 1.0 BE D:BEF1002 3.3 75.2 1.0 NH1 D:ARG212 3.5 50.5 1.0 CG2 D:THR185 3.6 73.7 1.0 O2A D:ADP1000 3.7 59.4 1.0 OE2 D:GLU215 3.8 50.1 1.0 N D:THR185 3.8 71.5 1.0 CA D:THR185 3.8 72.4 1.0 F2 D:BEF1002 4.0 72.3 1.0 O1B D:ADP1000 4.1 52.0 1.0 O3A D:ADP1000 4.2 56.8 1.0 OE1 D:GLU215 4.3 47.3 1.0 PA D:ADP1000 4.3 59.6 1.0 OD2 D:ASP265 4.4 55.6 1.0 CD D:GLU215 4.4 49.6 1.0 F1 D:BEF1002 4.4 75.9 1.0 NZ D:LYS184 4.5 46.9 1.0 NH2 E:ARG366 4.5 55.1 1.0 O1A D:ADP1000 4.7 60.1 1.0 CZ D:ARG212 4.7 51.4 1.0 OD1 D:ASP265 4.7 52.1 1.0 OE2 D:GLU211 4.9 66.0 1.0 C D:THR185 4.9 75.1 1.0

Magnesium binding site 5 out of 5 in the Rho Transcription Termination Factor Bound to RU8 and 5 Adp-BEF3 Molecules


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Rho Transcription Termination Factor Bound to RU8 and 5 Adp-BEF3 Molecules within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg1001 b:64.1 occ:1.00 F3 F:BEF1002 1.9 67.8 1.0 O2B F:ADP1000 2.0 93.3 1.0 O F:HOH1101 2.2 88.6 1.0 OG1 F:THR185 2.2 68.4 1.0 O F:HOH1103 2.2 80.5 1.0 O F:HOH1102 2.4 97.0 1.0 PB F:ADP1000 3.0 93.5 1.0 O1B F:ADP1000 3.1 93.0 1.0 BE F:BEF1002 3.3 68.0 1.0 CB F:THR185 3.3 68.9 1.0 O1A F:ADP1000 3.7 93.2 1.0 N F:THR185 3.9 69.7 1.0 F2 F:BEF1002 4.0 68.3 1.0 OD2 F:ASP265 4.0 80.5 1.0 O3B F:ADP1000 4.1 93.9 1.0 CA F:THR185 4.1 69.5 1.0 O3A F:ADP1000 4.2 93.9 1.0 OD1 F:ASP265 4.3 80.5 1.0 PA F:ADP1000 4.3 93.8 1.0 F1 F:BEF1002 4.4 67.9 1.0 CG2 F:THR185 4.5 68.9 1.0 OE2 F:GLU215 4.5 64.7 1.0 OE1 F:GLU215 4.5 64.7 1.0 CG F:ASP265 4.6 80.6 1.0 NH1 F:ARG212 4.6 73.0 1.0 O2A F:ADP1000 4.7 94.3 1.0 OE2 F:GLU211 4.8 81.7 1.0 CD F:GLU215 4.9 64.7 1.0 CB F:LYS184 4.9 66.1 1.0 OE1 F:GLU211 4.9 82.1 1.0 CD F:GLU211 4.9 81.9 1.0 NZ F:LYS184 4.9 65.4 1.0 C F:LYS184 5.0 66.3 1.0

N.D.Thomsen, M.R.Lawson, L.B.Witkowsky, S.Qu, J.M.Berger. Molecular Mechanisms of Substrate-Controlled Ring Dynamics and Substepping in A Nucleic Acid-Dependent Hexameric Motor. Proc. Natl. Acad. Sci. V. 113 E7691 2016U.S.A..
ISSN: ESSN 1091-6490
PubMed: 27856760
DOI: 10.1073/PNAS.1616745113